Lecture 10 - Enzyme Catalyse a reaction

Question 1

Strategies for Catalysis (6)

Answer 1

1. Acid-base catalysis
2. Covalent catalysis
3. Redox and radical catalysis (metal ions)
4. Geometric effects (proximity and orientation)
5. Stabilisation of the transition state
6. Cofactors with activated groups, e.g. electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2).

Question 2

Do many enzymes use more than one from the strategies for catalysis list?

Answer 2

Yes
not exclusive
not exhaustive

Question 3

For two molecules to react they need to be:

Answer 3

Close together

right orientation

Question 4

Covalent catalysis

Answer 4

Involves formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme.

Question 5

what drives covalent catalysis?

Answer 5

Nucleophilic attack on an electrophile

Question 6

Good electrophiles

Answer 6

Positive

Centres that able to form additional bonds

Question 7

Good electrophiles examples

Answer 7

Carbonyl carbon atom
Cationic imine (Schiff base)

Question 8

Good nucleophiles

Answer 8

Things that attack electrophiles

Question 9

Good nucleophiles examples

Answer 9

Hydroxyl group (need to be deprotonated)
Sulfhydryl group (need to be deprotonated)
Amino group (uncharged state)
Imidazole group (uncharged state)
Found in enzyme active sites

Question 10

what does a nucleophilic attack require?

Answer 10

correct orientation

Ionisation

Question 11

acid-base catalysis

Answer 11

Involves ionisable groups and proton transfer.

Question 12

what may be part of the activation to the transition state?

Answer 12

Ionisation

Question 13

why do Groups need to be in correct ionisation state?

Answer 13

For catalytic mechanism to proceed.

Question 14

Ionisable group that can easily lose a proton

Answer 14

Glu

Asp

Question 15

Ionisable group that can easily gain a proton

Answer 15

Lys

Arg

Question 16

Ionisable groups that most active in acid base catalysis and assist with forming better nucleophiles

Answer 16

Glu Asp

Lys Arg

Question 17

Enzyme activity is

Answer 17

pH dependent.

Question 18

what do each enzyme have at which its rate is highest?

Answer 18

characteristic optimal pH

Question 19

what do Amino acid sidechains need to be in?

Answer 19

correct ionisation state for catalytic mechanism to proceed.

Question 20

what example is suitable to acid base catalysis, types of reactions?

Answer 20

Histidine

Question 21

Histidine

Imidazole pKa

Answer 21

~ 6.5 – close to physiological pH

Question 22

what can the active site His depending on environment do?

Answer 22

Donate or accept proton

Question 23

Divergent evolution of serine proteases

incl examples

Answer 23

Same structure, unique specificities (pocket)

Chymotrypsin, Trypsin, Elastase

Question 24

Convergent evolution of serine proteases

Answer 24

Same catalytic triad occurs in different order and in different structures.

Question 25

Catalytic triad

Answer 25

Asp, his, ser Convergent evolution Occur in 3 different order and structure in 3 different proteins

Question 26

In Chymotrypsin: acid - base and covalent catalysis. what does the Catalytic triad comprise of?

Answer 26

serine, histidine and aspartic acid.

Question 27

In Chymotrypsin: acid - base and covalent catalysis. How does Serine Hydroxyl become a good nucleophile?

Answer 27

Sharing proton with histidine

Question 28

In Chymotrypsin: acid - base and covalent catalysis. What does Serine Hydroxyl attack?

Answer 28

Scissile bond

Question 29

In Chymotrypsin: acid - base and covalent catalysis. What does the Oxyanion hole do?

Answer 29

Stabilise tetrahedral intermediate

Question 30

In Chymotrypsin: acid - base and covalent catalysis. what is polarised by Asp102?

Answer 30

His57

Question 31

In Chymotrypsin: acid - base and covalent catalysis. what does His57 withdraw proton from?

Answer 31

Ser195 | becomes nucleophilic

Question 32

In Chymotrypsin: acid - base and covalent catalysis. what does Non-polar environment of Asp102 do?

Answer 32

raises its pKa. Oxyanion hole stabilise tetrahedral intermediate.

Question 33

In Chymotrypsin: acid - base and covalent catalysis. What drives decomposing of tetrahedral intermediate?

Answer 33

acid catalysis from His57.

Question 34

In Chymotrypsin: acid - base and covalent catalysis. what happens to both halves of polypeptide ‘acyl-enzyme intermediate’?

Answer 34

Half polypeptide remains covalently attached to the enzyme. other half can leave the active site.

Question 35

In Chymotrypsin: acid - base and covalent catalysis. what replaces one of the products in the active site in Acyl-enzyme intermediate?

Answer 35

Water

Question 36

In Chymotrypsin: acid - base and covalent catalysis. what is Polarised by His57 as a general base?

Answer 36

water

Question 37

In Chymotrypsin: acid - base and covalent catalysis. what does water make?

Answer 37

nucleophilic attack

Question 38

In Chymotrypsin: acid - base and covalent catalysis. | when water makes a nucleophilic attack what does it form? incl how its stabilised

Answer 38

second tetrahedral intermediate Stabilised by oxyanion hole

Question 39

In Chymotrypsin: acid - base and covalent catalysis. what acts as acid when 2nd intermediate decays?

Answer 39

His57

Question 40

In Chymotrypsin: acid - base and covalent catalysis. what does 2nd intermediate form when it decays?

Answer 40

Carboxylate

Question 41

In Chymotrypsin: acid - base and covalent catalysis. what happens when 2nd intermediate decays?

Answer 41

2nd product leave the active site. Active site has been regenerated and is ready for another round of catalysis.

Question 42

Aspartic protease mechanism examples

Answer 42

HIV protease and pepsin

Question 43

what is versatile?

Answer 43

Acid-base catalysis

Question 44

Catalytic triad occurs by

Answer 44

convergent and | divergent evolution.

Question 45

Stabilisation of electrophilic targets invites

Answer 45

nucleophilic attack.

Question 46

Stabilisation of an intermediate is

Answer 46

crucial to many reactions.

Question 47

Covalent catalysis can be resolved by

Answer 47

complementary half reaction.